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Long non-coding mRNA

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https://www.readbyqxmd.com/read/27932875/screening-of-long-non-coding-rna-and-tug1-inhibits-proliferation-with-tgf-%C3%AE-induction-in-patients-with-copd
#1
Wenxiang Tang, Zhenyu Shen, Jiang Guo, Shenghua Sun
OBJECTIVE: To evaluate differentially expressed long noncoding RNAs (lncRNAs) and the potential role of lncRNA TUG1 in patients with chronic obstructive pulmonary disease (COPD). METHODS: Total RNA was extracted from both COPD and non-COPD lung tissues, and microarray analysis was performed with 25,628 lncRNA probes and 20,106 mRNA probes. In addition, five up-regulated and five down-regulated lncRNAs were selected for identification using quantitative real-time polymerase chain reaction...
2016: International Journal of Chronic Obstructive Pulmonary Disease
https://www.readbyqxmd.com/read/27930710/urb-rip-an-adaptable-and-efficient-approach-for-immunoprecipitation-of-rnas-and-associated-rnas-proteins
#2
Kyle A Cottrell, Sergej Djuranovic
Post-transcriptional regulation of gene expression is an important process that is mediated by interactions between mRNAs and RNA binding proteins (RBP), non-coding RNAs (ncRNA) or ribonucleoproteins (RNP). Key to the study of post-transcriptional regulation of mRNAs and the function of ncRNAs such as long non-coding RNAs (lncRNAs) is an understanding of what factors are interacting with these transcripts. While several techniques exist for the enrichment of a transcript whether it is an mRNA or an ncRNA, many of these techniques are cumbersome or limited in their application...
2016: PloS One
https://www.readbyqxmd.com/read/27904771/tumor-suppressive-function-of-long-noncoding-rna-malat1-in-glioma-cells-by-suppressing-mir-155-expression-and-activating-fbxw7-function
#3
Shuanzhu Cao, Yanzhou Wang, Jinquan Li, Mingliang Lv, Haitao Niu, Yong Tian
The human metastasis associated lung adenocarcinoma transcript 1 (MALAT1) is a long non-coding RNA associated with metastasis, and is a favorable prognostic factor for lung cancer. Recent studies have shown that MALAT1 plays an important role in many malignancies. However, little is known about the role of MALAT1 in glioma. In this study, we determined the expression of MALAT1 and explored its prognostic value in glioma. Further, we investigated the regulatory mechanism of MALAT1 in glioma progression. Our results showed that the expression of MALAT1 was significantly decreased in glioma specimens than in noncancerous brain tissues...
2016: American Journal of Cancer Research
https://www.readbyqxmd.com/read/27904675/expression-of-long-non-coding-rna-hotair-in-oral-squamous-cell-carcinoma-tca8113-cells-and-its-associated-biological-behavior
#4
Huawei Liu, Zhiyong Li, Chao Wang, Lin Feng, Haitao Huang, Changkui Liu, Fengxia Li
As a long noncoding RNA, HOX transcript antisense intergenic RNA (HOTAIR) is highly expressed in many types of tumors. However, its expression and function in oral squamous cell carcinoma (OSCC) cells and tissues remains largely unknown. We herein studied the biological functions of HOTAIR in OSCC Tca8113 cells. Real-time quantitative PCR showed that HOTAIR, p21 and p53 mRNA expressions in doxorubicin (DOX)-treated or γ-ray-irradiated Tca8113 cells were up-regulated. Knockdown of p53 expression inhibited DOX-induced HOTAIR up-regulation, suggesting that DNA damage-induced HOTAIR expression may be associated with p53...
2016: American Journal of Translational Research
https://www.readbyqxmd.com/read/27902487/identification-of-laryngeal-cancer-prognostic-biomarkers-using-an-inflammatory-gene-related-competitive-endogenous-rna-network
#5
Qun He, Linli Tian, Hao Jiang, Jiarui Zhang, Qiang Li, Yanan Sun, Jiannan Zhao, Huijun Li, Ming Liu
Competitive endogenous RNAs (ceRNAs) act as molecular sponges for microRNAs (miRNAs), and are associated with tumorigenesis in various cancers, including laryngeal cancer (LC). In this work, we constructed an LC-specific inflammatory gene-related ceRNA network (IceNet). In IceNet, ceRNAs targeting inflammation-related genes tended to be network hubs. Additionally, the betweenness centralities of these hub ceRNAs were higher than those of the inflammation-related genes themselves, indicating that the hub ceRNAs in this study played critical roles in communication between IceNet molecules...
November 25, 2016: Oncotarget
https://www.readbyqxmd.com/read/27893425/tag-snps-of-long-non-coding-rna-tincr-affect-the-genetic-susceptibility-to-gastric-cancer-in-a-chinese-population
#6
Xiang Ma, Chi Huang, Dakui Luo, Younan Wang, Ran Tang, Xiangkun Huan, Yi Zhu, Zekuan Xu, Ping Liu, Li Yang
Tissue differentiation-inducing non-protein coding RNA (TINCR) is required for normal epidermal differentiation. TINCR is also strongly overexpressed in human gastric cancer (GC) and contributes to carcinogenesis and tumor progression. However, the association between TINCR polymorphisms and the risk of any diseases, such as GC, remains unknown. In the present study, the tag single nucleotide polymorphisms rs8113645, rs2288947, rs8105637, and rs12610531 were analyzed in 602 patients with GC and 602 age- and sex-matched controls...
November 23, 2016: Oncotarget
https://www.readbyqxmd.com/read/27891097/molecular-characterization-of-aquaporin-1-and-aquaporin-3-from-the-gills-of-the-african-lungfish-protopterus-annectens-and-changes-in-their-branchial-mrna-expression-levels-and-protein-abundance-during-three-phases-of-aestivation
#7
You R Chng, Jasmine L Y Ong, Biyun Ching, Xiu L Chen, Kum C Hiong, Wai P Wong, Shit F Chew, Siew H Lam, Yuen K Ip
African lungfishes can undergo long periods of aestivation on land during drought. During aestivation, lungfishes are confronted with desiccation and dehydration, and their gills become non-functional and covered with a thick layer of dried mucus. Aquaporins (Aqps) are a superfamily of integral membrane proteins which generally facilitate the permeation of water through plasma membranes. This study aimed to obtain the complete cDNA coding sequences of aqp1 and aqp3 from the gills of Protopterus annectens, and to determine their branchial mRNA and protein expression levels during the induction, maintenance and arousal phases of aestivation...
2016: Frontiers in Physiology
https://www.readbyqxmd.com/read/27889980/-the-importance-of-free-nucleic-acids-in-the-non-invasive-diagnostics
#8
Bálint Nagy, Zoltán Csanádi, Róbert Póka
There is a great interest to determine the physiological role of "free" nucleic acids, and to use them in the clinical diagnostics. These could be DNA, mRNA, microRNA and long non-coding RNA molecules, they are in the body fluids, like serum, tear, saliva, etc. Their exact role in the normal and pathological physiological processes is still in the focus of the research, while their use in the diagnostics is becoming more and more important. The use of "free" DNA in the non-invasive prenatal diagnosis is the first clinical application of the new generation sequencers, these methods are able to reach 99...
November 2016: Orvosi Hetilap
https://www.readbyqxmd.com/read/27887846/long-non-coding-rna-metastasis-associated-lung-adenocarcinoma-transcript-1-regulates-the-expression-of-gli2-by-mir-202-to-strengthen-gastric-cancer-progression
#9
Yue Zhang, Zhuo Chen, Ming-Jing Li, Huan-Yu Guo, Nian-Cai Jing
BACKGROUND: Gastric cancer (GC) is one of the most common malignancies and ranks the second leading cause of cancer death worldwide. Some studies had reported the tumor-promoting effects of long non-coding RNA metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) as a competing endogenous RNA (ceRNA) by sponging to microRNAs. However, the molecular mechanism of ceRNA regulatory pathway involving MALAT1 in GC remains unclear. METHODS: MALAT1 and miR -202 expression was detected by quantitative real time PCR (qRT-PCR) in 60 gastric cancer tissues and adjacent normal tissues, CCK8 cell proliferation assays, cell cycle analysis and cell apoptosis assays were performed to detect the GC cell proliferation and apoptosis...
November 22, 2016: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/27872686/engineering-translation-in-mammalian-cell-factories-to-increase-protein-yield-the-unexpected-use-of-long-non-coding-sineup-rnas
#10
REVIEW
Silvia Zucchelli, Laura Patrucco, Francesca Persichetti, Stefano Gustincich, Diego Cotella
Mammalian cells are an indispensable tool for the production of recombinant proteins in contexts where function depends on post-translational modifications. Among them, Chinese Hamster Ovary (CHO) cells are the primary factories for the production of therapeutic proteins, including monoclonal antibodies (MAbs). To improve expression and stability, several methodologies have been adopted, including methods based on media formulation, selective pressure and cell- or vector engineering. This review presents current approaches aimed at improving mammalian cell factories that are based on the enhancement of translation...
2016: Computational and Structural Biotechnology Journal
https://www.readbyqxmd.com/read/27869204/mrna-changes-in-nucleus-accumbens-related-to-methamphetamine-addiction-in-mice
#11
Li Zhu, Jiaqi Li, Nan Dong, Fanglin Guan, Yufeng Liu, Dongliang Ma, Eyleen L K Goh, Teng Chen
Methamphetamine (METH) is a highly addictive psychostimulant that elicits aberrant changes in the expression of microRNAs (miRNAs) and long non-coding RNAs (lncRNAs) in the nucleus accumbens of mice, indicating a potential role of METH in post-transcriptional regulations. To decipher the potential consequences of these post-transcriptional regulations in response to METH, we performed strand-specific RNA sequencing (ssRNA-Seq) to identify alterations in mRNA expression and their alternative splicing in the nucleus accumbens of mice following exposure to METH...
November 21, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27864543/long-non-coding-rnas-a-novel-paradigm-for-toxicology
#12
REVIEW
Joseph L Dempsey, Julia Yue Cui
Long non-coding RNAs (lncRNAs) are over 200 nucleotides in length and are transcribed from the mammalian genome in a tissue-specific and developmentally regulated pattern. There is growing recognition that lncRNAs are novel biomarkers and/or key regulators of toxicological responses in humans and animal models. Lacking protein-coding capacity, the numerous types of lncRNAs possess a myriad of transcriptional regulatory functions that include cis and trans gene expression, transcription factor activity, chromatin remodeling, imprinting, and enhancer up-regulation...
November 17, 2016: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/27864472/transcriptome-wide-identification-of-nmd-targeted-human-mrnas-reveals-extensive-redundancy-between-smg6-and-smg7-mediated-degradation-pathways
#13
Martino Colombo, Evangelos D Karousis, Joël Bourquin, Rémy Bruggmann, Oliver Mühlemann
Besides degrading aberrant mRNAs that harbor a premature translation termination codon (PTC), nonsense-mediated mRNA decay (NMD) also targets many seemingly "normal" mRNAs that encode for full-length proteins. To identify a bona fide set of such endogenous NMD targets in human cells, we applied a meta-analysis approach in which we combined transcriptome profiling of knockdowns and rescues of the three NMD factors UPF1, SMG6 and SMG7. We provide evidence that this combinatorial approach identifies NMD-targeted transcripts more reliably than previous attempts that focused on inactivation of single NMD factors...
November 18, 2016: RNA
https://www.readbyqxmd.com/read/27863467/microarray-analysis-reveals-a-potential-role-of-lncrnas-expression-in-cardiac-cell-proliferation
#14
Jue Wang, Zhimin Geng, Jiakan Weng, Longjie Shen, Ming Li, Xueli Cai, Chengchao Sun, Maoping Chu
BACKGROUND: Long non-coding RNAs (LncRNAs) have been identified to play important roles in epigenetic processes that underpin organogenesis. However, the role of LncRNAs in the regulation of transition from fetal to adult life of human heart has not been evaluated. METHODS: Immunofiuorescent staining was used to determine the extent of cardiac cell proliferation. Human LncRNA microarrays were applied to define gene expression signatures of the fetal (13-17 weeks of gestation, n = 4) and adult hearts (30-40 years old, n = 4)...
November 18, 2016: BMC Developmental Biology
https://www.readbyqxmd.com/read/27862640/long-non-coding-rna-malat1-functions-as-a-mediator-in-cardioprotective-effects-of-fentanyl-in-myocardial-ischemia-reperfusion-injury
#15
Zhi-Hui Zhao, Wei Hao, Qing-Tao Meng, Xiao-Bing Du, Shao-Qing Lei, Zhong-Yuan Xia
Long non-coding (lncRNA) MALAT1 can be increased by hypoxia or ischemic limbs. Also downregulation of MALAT1 contributes to reduction of cardiomyocyte apoptosis. However, the functional involvement of MALAT1 in myocardial ischemia-reperfusion (I/R) injury has not been defined. This study investigated the functional involvement of lncRNA-MALAT1 in cardioprotective effects of fentanyl. HL-1, a cardiac muscle cell line from the AT-1 mouse atrial cardiomyocyte tumor lineage, was pre-treated with fentanyl and generated cell model of hypoxia-reoxygenation (H/R)...
November 9, 2016: Cell Biology International
https://www.readbyqxmd.com/read/27862469/araport11-a-complete-reannotation-of-the-arabidopsis-thaliana-reference-genome
#16
Chia-Yi Cheng, Vivek Krishnakumar, Agnes Chan, Françoise Thibaud-Nissen, Seth Schobel, Christopher D Town
The flowering plant Arabidopsis thaliana is a dicot model organism for research in many aspects of plant biology. A comprehensive annotation of its genome paves the way for understanding the functions and activities of all types of transcripts, including mRNA, the various classes of non-coding RNA, and small RNA. The TAIR10 annotation update had a profound impact on Arabidopsis research but was released more than five years ago. Maintaining the accuracy of the annotation continues to be a prerequisite for future progress...
November 8, 2016: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/27849024/analysis-of-microarray-data-on-gene-expression-and-methylation-to-identify-long-non-coding-rnas-in-non-small-cell-lung-cancer
#17
Nannan Feng, Travers Ching, Yu Wang, Ben Liu, Hongyan Lin, Oumin Shi, Xiaohong Zhang, Min Zheng, Xin Zheng, Ming Gao, Zhi-Jie Zheng, Herbert Yu, Lana Garmire, Biyun Qian
To identify what long non-coding RNAs (lncRNAs) are involved in non-small cell lung cancer (NSCLC), we analyzed microarray data on gene expression and methylation. Gene expression chip and HumanMethylation450BeadChip were used to interrogate genome-wide expression and methylation in tumor samples. Differential expression and methylation were analyzed through comparing tumors with adjacent non-tumor tissues. LncRNAs expressed differentially and correlated with coding genes and DNA methylation were validated in additional tumor samples using RT-qPCR and pyrosequencing...
November 16, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27835598/snhg8-is-identified-as-a-key-regulator-of-epstein-barr-virus-ebv-associated-gastric-cancer-by-an-integrative-analysis-of-lncrna-and-mrna-expression
#18
Tao Huang, Yan Ji, Dan Hu, Baozheng Chen, Hejun Zhang, Chao Li, Gang Chen, Xingguang Luo, Xiong-Wei Zheng, Xiandong Lin
The Epstein-Barr virus (EBV) is associated with a variety of cancers, including gastric cancer, which has one of the highest mortality rates of all human cancers. Long non-coding RNAs (lncRNAs) have been suggested to have important causal roles in gastric cancer. However, the interaction between lncRNAs and EBV has not yet been studied. To this end, we sequenced 11,311 lncRNAs and 144,826 protein-coding transcripts from four types of tissue: one non-EBV-infected gastric carcinoma (EBVnGC) and its adjacent normal tissue, and one EBV-associated gastric carcinoma (EBVaGC) and its adjacent normal tissue...
November 7, 2016: Oncotarget
https://www.readbyqxmd.com/read/27829996/down-regulation-of-long-non-coding-rna-foxd3-antisense-rna-1-foxd3-as1-inhibits-cell-proliferation-migration-and-invasion-in-malignant-glioma-cells
#19
Zhen-Hua Chen, Hong-Kang Hu, Chen-Ran Zhang, Cheng-Yin Lu, Yi Bao, Zheng Cai, Yong-Xiang Zou, Guo-Han Hu, Lei Jiang
Growing evidence indicates that long non-coding RNAs (lncRNAs) play key roles in cancer initiation and progression. However, little is known about the therapeutic significance of lncRNAs in glioma. In this study, we explored the tumorigenic role of a classical lncRNA, FOXD3 antisense RNA 1 (FOXD3-AS1) in glioma. Systemic analysis of the patient specimens and clinical data showed that FOXD3-AS1 was markedly up-regulated in high-grade glioma tissues (WHO grade III-IV) compared with that in low-grade glioma (WHO grade I-II) and normal brain tissues (both P<0...
2016: American Journal of Translational Research
https://www.readbyqxmd.com/read/27826625/integrated-analysis-of-long-non-coding-rna%C3%A2-associated-cerna-network-reveals-potential-lncrna-biomarkers-in-human-lung-adenocarcinoma
#20
Jing Sui, Yun-Hui Li, Yan-Qiu Zhang, Cheng-Yun Li, Xian Shen, Wen-Zhuo Yao, Hui Peng, Wei-Wei Hong, Li-Hong Yin, Yue-Pu Pu, Ge-Yu Liang
Accumulating evidence has highlighted the important roles of long non-coding RNAs (lncRNAs) acting as competing endogenous RNAs (ceRNAs) in tumor biology. However, the roles of cancer specific lncRNAs in lncRNA-related ceRNA network of lung adenocarcinoma (LUAD) are still unclear. In the present study, the 465 RNA sequencing profiles in LUAD patients were obtained from the cancer genome atlas (TCGA) database, which provides large sample RNA sequencing data free of charge, and 41 cancer specific lncRNAs, 25 miRNAs and 1053 mRNAs (fold change >2, p<0...
November 2016: International Journal of Oncology
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